Lorena Pantano: Transitioning through the nf-core era at the Harvard Chan Bioinformatics Core


The Harvard Chan Bioinformatics Core is dedicated to fostering collaboration within the Life Sciences, aiming to expedite research endeavors using innovative and proven methodologies for high-throughput sequencing data. In 2011, in response to the absence of a globally adaptable workflow manager at the time, Brad Chapman began developing Bcbio, a Python-based NGS workflow manager, for the Core. Bcbio, which synthesizes insights learned from numerous projects to provide best-practice workflows, gained traction within and beyond the Core and has been embraced by academic researchers, hospitals, and industry alike. Continuously adapting to meet the evolving demands of diverse infrastructure architectures, Bcbio has faced the ongoing challenge of remaining current and adaptable. Over the past five years, the nf-core community has harnessed the capabilities of Nextflow as a workflow manager, fostering the creation of an international, open-source ecosystem supporting over 50 pipelines. As ambassadors of analysis reproducibility and scalability, the Harvard Chan Bioinformatics Core recognizes the imperative of transitioning to nf-core, albeit a complex process in our organization. In this presentation, we outline the rationale behind this migration, elucidate the challenges we are encountering, and delineate our roadmap toward community-wide adoption, drawing upon our experiences with the Bcbio platform.

May 23, 2024 2:15 PM